# Noisy PMF when pulling metal ion from a protein

**URL:** <https://gromacs.bioexcel.eu/t/noisy-pmf-when-pulling-metal-ion-from-a-protein/7453>\
**Category:** User discussions\
**Created:** [October 23, 2023, 4:50am UTC](https://gromacs.bioexcel.eu/t/noisy-pmf-when-pulling-metal-ion-from-a-protein/7453 "2023-10-23T04:50:48Z")\
**Posts on this page:** 5\
**Page:** 1

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**Author:** ![rajas](https://avatars.discourse-cdn.com/v4/letter/r/ea5d25/32.png) [@rajas](https://gromacs.bioexcel.eu/u/rajas)\
**Post date:** [October 23, 2023, 4:50am UTC](https://gromacs.bioexcel.eu/t/noisy-pmf-when-pulling-metal-ion-from-a-protein/7453/1 "2023-10-23T04:50:48Z")

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GROMACS version:2022.5  
GROMACS modification: Yes (plumed 2.9.0)  
Dear gromacs users,  
I am trying to pull a calcium ion from a metal-protein complex to find the unbinding energy using charmm36 ff. The simulation went smooth and the pulling force looks reasonable (mdp parameters are very similar to Justin’s umbrella sampling tutorial). However, PMF at the early stage of the pulling is very noisy. I am missing something here to understand and correct this, unfortunately still unable to catch it. Any help to understand this is appreciated.  
 ![image](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/e/ecf4cf8b5b54e6f8c4b1bf5b534e73b7669f0f69.png)

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**Author:** ![obZehn](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/obzehn/32/2629_2.png) [@obZehn](https://gromacs.bioexcel.eu/u/obZehn)\
**Post date:** [November 14, 2023, 10:15am UTC](https://gromacs.bioexcel.eu/t/noisy-pmf-when-pulling-metal-ion-from-a-protein/7453/2 "2023-11-14T10:15:33Z")

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How did you calculate the PMF? I don’t understand what it the ‘Umbrella Potential’ you are plotting.

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**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\
**Post date:** [November 14, 2023, 1:38pm UTC](https://gromacs.bioexcel.eu/t/noisy-pmf-when-pulling-metal-ion-from-a-protein/7453/3 "2023-11-14T13:38:02Z")

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That’s just the default title printed by `gmx wham`. Perhaps a bit misleading, but what’s shown is the free energy surface.

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**Author:** ![rajas](https://avatars.discourse-cdn.com/v4/letter/r/ea5d25/32.png) [@rajas](https://gromacs.bioexcel.eu/u/rajas)\
**Post date:** [November 22, 2023, 10:14am UTC](https://gromacs.bioexcel.eu/t/noisy-pmf-when-pulling-metal-ion-from-a-protein/7453/4 "2023-11-22T10:14:10Z")

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Yes, Justin is correct, it is a free energy curve. Sorry for the misleading figure title.

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**Author:** ![MagnusL](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/magnusl/32/2380_2.png) [@MagnusL](https://gromacs.bioexcel.eu/u/MagnusL)\
**Post date:** [November 24, 2023, 1:45pm UTC](https://gromacs.bioexcel.eu/t/noisy-pmf-when-pulling-metal-ion-from-a-protein/7453/5 "2023-11-24T13:45:39Z")

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I don’t know the exact settings you have used, but my assumption would be that sampling the unbinding of a calcium ion might require tighter placed sampling windows with higher pull force constant than what was used in the tutorial you based your simulations on. You would probably also need to simulate longer in each of the sampling simulations.

Have you checked the histogram overlap from `gmx wham`?